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MicroED structure of papain complexed with natural product E-64-A65 from microcrystals soaked in crude biosynthetic reaction mixture
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9PAP
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.2 α = 90 b = 48.78 β = 90 c = 100.1 γ = 90
Symmetry Space Group P 21 21 21
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT FREE R-VALUE 2.5 50.05 1.34 6554 656 86.45 0.1847 0.1797 0.2138 0.2277 0.2593
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.249 f_angle_d 1.119 f_chiral_restr 0.074 f_plane_restr 0.009 f_bond_d 0.007
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing
Sample Papain-E64-A65 complex
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) 2.5 Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 42.2 Length b 48.78 Length c 48.78 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 (9PAP) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type DIRECT ELECTRON APOLLO (4k x 4k) Electron Dose (electrons/Å**2) 0.045
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS TALOS F200C Minimum Defocus (nm) 10000 Maximum Defocus (nm) 10000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode DIFFRACTION Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE